Improved log-Gaussian approximation for over-dispersed Poisson regression: Application to spatial analysis of COVID-19.
Ontology highlight
ABSTRACT:
SUBMITTER: Murakami D
PROVIDER: S-EPMC8741021 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The rapid worldwide evolution of LEDs as light sources has brought new challenges, which means that new methods are needed and new algorithms have to be developed. Since the majority of LED luminaries are of the multi-source type, established methods for the design of light engines cannot be used in the design of LED light engines. This is because in the latter case what is involved is not just the design of a good reflector or projector lens, but the design of several lenses which have to work together in order to achieve satisfactory results. Since lenses can also be bought off the shelf from several manufacturers, it should be possible to combine together different off the shelf lenses in order to design a good light engine. However, with so many different lenses to choose from, it is almost impossible to find an optimal combination by hand, which means that some optimization algorithms need to be applied. In order for them to work properly, it is first necessary to describe the input data (i.e. spatial light distribution) in a functional form using as few as possible parameters. In this paper the focus is on the approximation of the input data, and the implementation of the well-known mathematical procedure for the separation of linear and nonlinear parameters, which can provide a substantial increase in performance.
| S-EPMC5409530 | biostudies-literature
Project description:BackgroundTsetse flies are the major vectors of human trypanosomiasis of the form Trypanosoma brucei rhodesiense and T.b.gambiense. They are widely spread across the sub-Saharan Africa and rendering a lot of challenges to both human and animal health. This stresses effective agricultural production and productivity in Africa. Delimiting the extent and magnitude of tsetse coverage has been a challenge over decades due to limited resources and unsatisfactory technology. In a bid to overcome these limitations, this study attempted to explore modelling skills that can be applied to spatially estimate tsetse abundance in the country using limited tsetse data and a set of remote-sensed environmental variables.MethodologyEntomological data for the period 2008-2018 as used in the model were obtained from various sources and systematically assembled using a structured protocol. Data harmonisation for the purposes of responsiveness and matching was carried out. The key tool for tsetse trapping was itemized as pyramidal trap in many instances and biconical trap in others. Based on the spatially explicit assembled data, we ran two regression models; standard Poisson and Zero-Inflated Poisson (ZIP), to explore the associations between tsetse abundance in Uganda and several environmental and climatic covariates. The covariate data were constituted largely by satellite sensor data in form of meteorological and vegetation surrogates in association with elevation and land cover data. We finally used the Zero-Inflated Poisson (ZIP) regression model to predict tsetse abundance due to its superiority over the standard Poisson after model fitting and testing using the Vuong Non-Nested statistic.ResultsA total of 1,187 tsetse sampling points were identified and considered as representative for the country. The model results indicated the significance and level of responsiveness of each covariate in influencing tsetse abundance across the study area. Woodland vegetation, elevation, temperature, rainfall, and dry season normalised difference vegetation index (NDVI) were important in determining tsetse abundance and spatial distribution at varied scales. The resultant prediction map shows scaled tsetse abundance with estimated fitted numbers ranging from 0 to 59 flies per trap per day (FTD). Tsetse abundance was found to be largest at low elevations, in areas of high vegetative activity, in game parks, forests and shrubs during the dry season. There was very limited responsiveness of selected predictors to tsetse abundance during the wet season, matching the known fact that tsetse disperse most significantly during wet season.ConclusionsA methodology was advanced to enable compilation of entomological data for 10 years, which supported the generation of tsetse abundance maps for Uganda through modelling. Our findings indicate the spatial distribution of the G. f. fuscipes as; low 0-5 FTD (48%), medium 5.1-35 FTD (18%) and high 35.1-60 FTD (34%) grounded on seasonality. This approach, amidst entomological data shortages due to limited resources and absence of expertise, can be adopted to enable mapping of the vector to provide better decision support towards designing and implementing targeted tsetse and tsetse-transmitted African trypanosomiasis control strategies.
| S-EPMC8648107 | biostudies-literature
Project description:We extend the blindspot model for self-supervised denoising to handle Poisson-Gaussian noise and introduce an improved training scheme that avoids hyperparameters and adapts the denoiser to the test data. Self-supervised models for denoising learn to denoise from only noisy data and do not require corresponding clean images, which are difficult or impossible to acquire in some application areas of interest such as low-light microscopy. We introduce a new training strategy to handle Poisson-Gaussian noise which is the standard noise model for microscope images. Our new strategy eliminates hyperparameters from the loss function, which is important in a self-supervised regime where no ground truth data is available to guide hyperparameter tuning. We show how our denoiser can be adapted to the test data to improve performance. Our evaluations on microscope image denoising benchmarks validate our approach.
| S-EPMC8294668 | biostudies-literature
Project description:Log-binomial and robust (modified) Poisson regression models are popular approaches to estimate risk ratios for binary response variables. Previous studies have shown that comparatively they produce similar point estimates and standard errors. However, their performance under model misspecification is poorly understood.In this simulation study, the statistical performance of the two models was compared when the log link function was misspecified or the response depended on predictors through a non-linear relationship (i.e. truncated response).Point estimates from log-binomial models were biased when the link function was misspecified or when the probability distribution of the response variable was truncated at the right tail. The percentage of truncated observations was positively associated with the presence of bias, and the bias was larger if the observations came from a population with a lower response rate given that the other parameters being examined were fixed. In contrast, point estimates from the robust Poisson models were unbiased.Under model misspecification, the robust Poisson model was generally preferable because it provided unbiased estimates of risk ratios.
| S-EPMC6013902 | biostudies-other
Project description:Working memory (WM) was one of the first cognitive processes studied with functional magnetic resonance imaging (fMRI). With now over 20 years of studies on WM, each study with tiny sample sizes, there is a need for meta-analysis to identify the brain regions consistently activated by WM tasks, and to understand the inter-study variation in those activations. However, current methods in the field cannot fully account for the spatial nature of neuroimaging meta-analysis data or the heterogeneity observed among WM studies. In this work, we propose a fully Bayesian random-effects meta-regression model based on log-Gaussian Cox processes, which can be used for meta-analysis of neuroimaging studies. An efficient MCMC scheme for posterior simulations is presented which makes use of some recent advances in parallel computing using graphics processing units (GPUs). Application of the proposed model to a real dataset provides valuable insights regarding the function of the WM.
| S-EPMC6430202 | biostudies-literature
Project description:Count data commonly arise in natural sciences but adequately modeling these data is challenging due to zero-inflation and over-dispersion. While multiple parametric modeling approaches have been proposed, unfortunately there is no consensus regarding how to choose the best model. In this article, we propose a ordinal regression model (MN) as a default model for count data given that this model is shown to fit well data that arise from several types of discrete distributions. We extend this model to allow for automatic model selection (MN-MS) and show that the MN-MS model generates superior inference when compared to using the full model or more traditional model selection approaches. The MN-MS model is used to determine how human biting rate of mosquitoes, known to be able to transmit malaria, are influenced by environmental factors in the Peruvian Amazon. The MN-MS model had one of the best fit and out-of-sample predictive skill amongst all models. While A. darlingi is strongly associated with highly anthropized landscapes, all the other mosquito species had higher mean biting rates in landscapes with a lower fraction of exposed soil and urban area, revealing a striking shift in species composition. We believe that the MN and MN-MS models are valuable additions to the modelling toolkit employed by environmental modelers and quantitative ecologists.
| S-EPMC6395857 | biostudies-literature
Project description:This study discusses the development of Zero Inflated Generalized Poisson Regression (ZIGPR) with two response variables, that is Bivariate ZIGPR (BZIGPR). The extension of the ZIGPR model by considering spatial factor called Geographically Weighted Zero Inflated Generalized Poisson Regression (GWBZIGPR). The GWBZIGPR produces a local parameter estimator for each location of observation. The parameter estimation using the Maximum Likelihood Estimation (MLE) method obtained an equation that did not closed-form so that the numerical iteration of Berndt Hall Hall Hausman (BHHH) is used. The data used in this study are the number of pregnant maternal mortality and postpartum maternal mortality data in 91 sub-districts in Pekalongan Residency, Central Java Province. The results showed that the Akaike Information Criterion Corrected (AICc) value in the GWBZIGPR model is smaller than BZIGPR, so it means that the GWBZIGPR is better than the BZIGPR for modeling the number of pregnant maternal mortality and postpartum maternal mortality in Pekalongan Residency. The results of this study will assist local governments in anticipating the causes of maternal mortality.
| S-EPMC8319482 | biostudies-literature
Project description:Event-related potentials (ERPs) summarize electrophysiological brain response to specific stimuli. They can be considered as correlated functions of time with both spatial correlation across electrodes and nested correlations within subjects. Commonly used analytical methods for ERPs often focus on pre-determined extracted components and/or ignore the correlation among electrodes or subjects, which can miss important insights, and tend to be sensitive to outlying subjects, time points or electrodes. Motivated by ERP data in a smoking cessation study, we introduce a Bayesian spatial functional regression framework that models the entire ERPs as spatially correlated functional responses and the stimulus types as covariates. This novel framework relies on mixed models to characterize the effects of stimuli while simultaneously accounting for the multilevel correlation structure. The spatial correlation among the ERP profiles is captured through basis-space Matérn assumptions that allow either separable or nonseparable spatial correlations over time. We induce both adaptive regularization over time and spatial smoothness across electrodes via a correlated normal-exponential-gamma (CNEG) prior on the fixed effect coefficient functions. Our proposed framework includes both Gaussian models as well as robust models using heavier-tailed distributions to make the regression automatically robust to outliers. We introduce predictive methods to select among Gaussian vs. robust models and models with separable vs. non-separable spatiotemporal correlation structures. Our proposed analysis produces global tests for stimuli effects across entire time (or time-frequency) and electrode domains, plus multiplicity-adjusted pointwise inference based on experiment-wise error rate or false discovery rate to flag spatiotemporal (or spatio-temporal-frequency) regions that characterize stimuli differences, and can also produce inference for any prespecified waveform components. Our analysis of the smoking cessation ERP data set reveals numerous effects across different types of visual stimuli.
| S-EPMC6139054 | biostudies-literature
Project description:The need for more pragmatic approaches to achieve sustainable development goal on childhood mortality reduction necessitated this study. Simultaneous study of the influence of where the children live and the censoring nature of children survival data is scarce. We identified the compositional and contextual factors associated with under-five (U5M) and infant (INM) mortality in Nigeria from 5 MCMC Bayesian hierarchical Poisson regression models as approximations of the Cox survival regression model. The 2018 DHS data of 33,924 under-five children were used. Life table techniques and the Mlwin 3.05 module for the analysis of hierarchical data were implemented in Stata Version 16. The overall INM rate (INMR) was 70 per 1000 livebirths compared with U5M rate (U5MR) of 131 per 1000 livebirth. The INMR was lowest in Ogun (17 per 1000 live births) and highest in Kaduna (106), Gombe (112) and Kebbi (116) while the lowest U5MR was found in Ogun (29) and highest in Jigawa (212) and Kebbi (248). The risks of INM and U5M were highest among children with none/low maternal education, multiple births, low birthweight, short birth interval, poorer households, when spouses decide on healthcare access, having a big problem getting to a healthcare facility, high community illiteracy level, and from states with a high proportion of the rural population in the fully adjusted model. Compared with the null model, 81% vs 13% and 59% vs 35% of the total variation in INM and U5M were explained by the state- and neighbourhood-level factors respectively. Infant- and under-five mortality in Nigeria is influenced by compositional and contextual factors. The Bayesian hierarchical Poisson regression model used in estimating the factors associated with childhood deaths in Nigeria fitted the survival data.
| S-EPMC8241837 | biostudies-literature
Project description:The log-rank test statistic is very broadly used in biology. Unfortunately, P-values based on the popular chi-square approximation are often inaccurate and can be misleading.
| S-EPMC6690426 | biostudies-literature